Assuming you are doing wet-jelqs, you are either:
(i) using little to no lube; if this is the case, use any number of lubes to make the process easier on the skin. Alternatively, you can change lubes. I found that I got a lot more out of olive oil than I did Vaseline.
(ii) stroking too hard thereby creating too much friction and thus resulting in the rawness or
(iii) some combination of the above.
If it’s dry jelqing, perhaps invest in a little bit of lube as Lazy Wally suggests or bring the reps down.
I find that jelqing is really a trial and error exercise. Some guys can jelq an incredible amount of reps while others (myself included) just find the exercise difficult to sustain for too long for due to some sort of sensitivity of the skin. Better to have a great mild session of 50 than an injurious session of 100, in my opinion. I know the newbie manual and other regimes talk about upping reps but I think that the timeframe in upping reps and by how much is determined by your own body, not what worked for someone else (physiology can be a bitch sometimes).
I have been there with the injuries from jelqing and I wish you a speedy recovery.